Related papers: A Model-Theoretic Approach to Modular Implementati…
State machine formalisms equipped with hierarchy and parallelism allow to compactly model complex system behaviours. Such models can then be transformed into executable code or inputs for model-based testing and verification techniques.…
A method of discovering how neurons are connected to process information is presented here: Design a simple logic circuit that can perform a single, biologically advantageous function. Engineering concepts can be helpful in choosing the…
Formation strategy is one of the most important parts of many multi-agent systems with many applications in real world problems. In this paper, a framework for learning this task in a limited domain (restricted environment) is proposed. In…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
In this paper, we further develop the framework of Modular Systems that lays model-theoretic foundations for combining different declarative languages, agents and solvers. We introduce a multi-language logic of modular systems. We define…
Requirements engineering plays a critical role in developing software systems. One of the most difficult tasks in this process is identifying functional requirements. A critical problem in many projects is missing requirements until late in…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…
Combinatorial evolution and forecasting of system requirements is examined. The morphological model is used for a hierarchical requirements system (i.e., system parts, design alternatives for the system parts, ordinal estimates for the…
We apply a compositional formal modeling and verification method to an autonomous aircraft taxi system. We provide insights into the modeling approach and we identify several research areas where further development is needed. Specifically,…
The contribution of this paper is threefold: first, it defines a framework for modelling component-based systems, as well as a formalization of integration rules to combine their behavior. This is based on finite state machines (FSM).…
Autonomous systems control many tasks in our daily lives. To increase trust in those systems and safety of the interaction between humans and autonomous systems, the system behaviour and reasons for autonomous decision should be explained…
In this paper, we propose a single-agent modal logic framework for reasoning about goal-direct "knowing how" based on ideas from linguistics, philosophy, modal logic and automated planning. We first define a modal language to express "I…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Although the biostatistical scientific literature publishes new methods at a very high rate, many of these developments are not trustworthy enough to be adopted by the scientific community. We propose a framework to think about how a piece…